CLEF is an MRC sponsored project in the E-Science programme that aims to establish policies and infrastructure for the next generation of integrated clinical and bioscience research. One of the major goals of the project is to provide a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies are needed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research.

To learn more about the overall approach adopted by CLEF to meet data protection requirements, including the data flows and pseudonymisation mechanisms that are currently being developed click here.

CLEF’s Goals:

• Enable secure and ethical collection of clinical information from multiple sites

• Analyse, structure, integrate, prioritise and disseminate

• Make resources available using GRID tools (e.g. ^myGrid )

• To provide access to clinical data to authorised clinicians and scientists

• Establish a secure and ethical framework for scientific collaboration

The Basic CLEF Information Flow

The requirements and technologies are best understood in the context of the CLEF information flow that has emerged from the design process and is shown in the figure below.

Starting with the “Patient care” at the bottom left of the diagram, the flow is:

· Capture of the information. Some information comes from dictated and transcribed text. Other information comes directly from hospital information systems – e.g. laboratory results, prescriptions, etc.

· Pseudonymisation of all information at the originating hospital by removal of overt identifying items – name, date of birth, etc - and by providing a CLEF Entry identifier that can only be reversed by the provider (or their nominated trusted third party)

· Depersonalisation of the texts to remove any residual information that might risk identification – e.g. names of relatives, nick names, place names, unusual occupations, etc. Hence a requirement for reliable scalable techniques.

· Information extraction of key information from the texts into predefined “templates”, possibly with the help of context provided by the information already in the repository hence the requirement for

· Integration into the health record repository of all information including laboratories, radiology, and genomic analyses

· Constructing the chronicle to infer a coherent view of the patient’s history. Typically the same information occurs in many different documents with different levels of granularity, clarity and sometimes conflicts that must be reconciled.

From this point the information can go in two directions:

· Use for patient care - back to the clinicians in the form of summaries for patient care.Providing a concise up-to-date summary of a patients’ condition is a prime request of clinicians for improving patient care. Because it requires re-identification of patients, this step can only occur at the hospital and after security controls have been stringently tested and agreed to be adequate.

Enrichment for E-Science – with the results of researchers’ queries, their workflows, interpretations, curation and links to external information added to the repository so that it becomes the basis for virtual communities of researchers.

CLEF Research

CLEF aims to develop rigorous generic methods for capturing and managing clinical information in patient care and for integrating that information into clinical and basic bioscience research.

CLEF will focus on cancer, but the goal is to produce a robust framework which can be used in many areas of clinical medicine and research based on emerging knowledge management techniques within the E-Science/Grids programme.

Click here for: Full Project Proposal

There is growing recognition that advances in health informatics are central both to the modernisation of health services and to successfully exploiting our rapidly expanding knowledge of genetics and molecular processes ('-omics'). Systems dealing with clinical information - what doctors, nurses and other healthcare professionals have heard, seen thought, and done - face major barriers in capturing information and assuring its quality. A more unified health service and more effective collaborative multidisciplinary research community both require significant progress in overcoming these barriers - as well as adapting the general e-Science issues of cooperation, integration, and dissemination to clinical needs. The scale, diversity and complexity of CLEF the problems require a coherent approach that draws on and contributes to the emerging common architectures and services of the e-Science/Grid communities.

CLEF’s specific objectives are:

† Develop security measures that support ethical information governance within the technical framework of the GRID and operational NHS systems

† Create information capture tools, and in particular language tools, to capture written medical records and enable their integration with digitized visual diagnostic and laboratory reports

† Build an integrated repository of information that directly support patient care

† Make its "Clinical E-Science Workbench" a widely accepted means for presenting clinical information and to integrate it with other information in the e-Science network

† Contribute to practical evaluation and further expansion of health informatics tools

The research will be embedded within the everyday large scale world of service delivery in a leading cancer institution (The Royal Marsden Hospital) and two cancer networks (in NC and NW London) of the NHS. It will draw on leading cancer research units (University College London), spanning the whole cycle of information management from genetics and structural biology to multicentre clinical trials and multiprofessional information systems for patients in primary care.

Though initially focusing on cancer, CLEF will be informed by the many research programmes of its participants in additional clinical fields such as in cardiovascular disease, genetics and neuroscience.

The outcomes of the project will be:

† Shared repositories integrating clinical, image and genomic information linked to medical records, literature and the Web.

† Information capture and language tools for clinical and scientific descriptions to populate the repositories and records.

† Information integration tools to bring together information from isolated studies and disparate medical records in the repositories and to facilitate constructing future studies and records to integrate smoothly into the repositories.

† Information display tools to make the information easily accessible, including where appropriate to patients and public.

† Knowledge management environments (the Clinical e-Science Workbench) to use the repositories to enhance biomedical research, based on generic architectures, and contributing to the relevant clinical and technical standards.

By the end of the project, the gap between our ability to manage and integrate clinical information and our ability to manage image and genomic information will have been significantly narrowed so that effective use can be made of the broader e-Science framework to benefit clinical research, patients, and public alike.

CLEF Services

The overall aim of CLEF Services Programme is to join up clinical care and post-genomic research. It aims to reduce the manual effort of managing clinical data for post-genomic research by improving clinical information capture and re-use and by improving usability, analysis and visualisation of the data.

CLEF Services will take the next steps towards deploying CLEF’s generic “horizontal” services as part of the health e-science GRID infrastructure to support vertical applications – clinical trials, longitudinal studies in specific clinical domains, first in cancer.

CLEF Services addresses issues encountered in CLEF in managing privacy and security and takes advantage of new opportunities provided by the advent of the NHS Spine. The NHS Spine is both an opportunity and a challenge for CLEF Services; an opportunity to acquire more patient information directly and a challenge to establish the policy level and technical links that will allow interworking between the academic/e-Science framework and the NHS National programme for IT (NPfIT). Links between the academic/e-Science infrastructure and the NHS are a prerequisite for realizing the potential of the NHS as a resource for clinical research.

The objectives of CLEF Services:

† Bring a multidisciplinary team to the key problems of privacy

† Package elements of the pilot scheme as GRID services and evaluate their use in the clinical centres

† Make its own results available within the e-Science framework and provide links to the underlying e-Science infrastructure for use by collaborators in vertical e-Science projects and in the National Cancer Research Institute (NCRI) Bioinformatics strategy

† Develop and pilot methodologies for inter-working between the new NHS Spine and the e-Science/GRID Infrastructure

† Move the emphasis form clinical data acquisition towards analysis, re-use and visualization

† Contribute nationally and internationally to standards for clinical information interchange, metadata and knowledge management

Long term vision:

† To enable faster and more effective clinical trials and experimental medical studies linking clinical and genomic information

† To allow more effective tailoring of care to individual patients

† To provide improved quality clinical information and reduce workload for clinicians

CLEF Services, which was launched in January 2005, will expand the clinical base for its developmental work. That will enable CLEF to begin to work with live data sets and step-up it's testing processes for user friendliness and faithfulness of data extraction and interpretation in face of complex queries.

Click here for: CLEF Services Proposal